Align C4-dicarboxylate TRAP transporter small permease protein DctQ (characterized, see rationale)
to candidate AZOBR_RS09600 AZOBR_RS09600 C4-dicarboxylate ABC transporter permease
Query= uniprot:Q9KQS0 (232 letters) >FitnessBrowser__azobra:AZOBR_RS09600 Length = 226 Score = 90.1 bits (222), Expect = 3e-23 Identities = 63/190 (33%), Positives = 90/190 (47%), Gaps = 35/190 (18%) Query: 26 DSIEEFLIAFFMGAMTLLTFANVIMRY----------LFNDNILWALEGTVFMFAWMVLV 75 D +EE LIAF M A T + F +V RY + + N+ WA E ++MF WM Sbjct: 5 DHLEEILIAFLMAAATTIIFISVAHRYAAGFPIIQDYILHWNLAWAQELCIYMFVWMAKF 64 Query: 76 GASFGVKRHFHIGVDVLINIAPARLRKLYALVAVACCLAFS-ILLLIGSWNYWHPFITER 134 GA++GV+ H+GVDVLIN LR + + + F+ ++ +GS WH Sbjct: 65 GAAYGVRTGIHVGVDVLINKLSTPLRAKFIVFGLLAGATFTGVVGTMGSTFVWH------ 118 Query: 135 AWYETDDIPMPDMLQFLADWVNEGERYEKLPRFIPYAALPIGMALLTFRFLQIAWQII-T 193 M D Q AD + P +I Y A+P+G L+ FRFLQ+ + T Sbjct: 119 ---------MSDTEQVSADL--------EWPMWIIYLAIPLGSYLMCFRFLQVMVNFLRT 161 Query: 194 GKLDRMIAGH 203 G+L GH Sbjct: 162 GELPHHDHGH 171 Lambda K H 0.329 0.140 0.447 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 168 Number of extensions: 13 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 232 Length of database: 226 Length adjustment: 23 Effective length of query: 209 Effective length of database: 203 Effective search space: 42427 Effective search space used: 42427 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory